gl2genepop: Converts a genlight object into genepop format (and file)

In dartR: Importing and Analysing 'SNP' and 'Silicodart' Data Generated by Genome-Wide Restriction Fragment Analysis

Converts a genlight object into genepop format (and file)

Description

The genepop format is used by several external applications (for example Neestimator2. So the main idea is to create the genepop file and then run the other software externally. As a feature, the genepop file is also returned as an invisible data.frame by the function.

Usage

gl2genepop(
  x,
  outfile = "genepop.gen",
  outpath = tempdir(),
  pop_order = "alphabetic",
  output_format = "2_digits",
  verbose = NULL
)

Arguments

x	Name of the genlight object containing the SNP data [required].
outfile	File name of the output file [default 'genepop.gen'].
outpath	Path where to save the output file. Use outpath=getwd() or outpath='.' when calling this function to direct output files to your working directory [default tempdir(), mandated by CRAN].
pop_order	Order of the output populations either "alphabetic" or a vector of population names in the order required by the user (see examples) [default "alphabetic"].
output_format	Whether to use a 2-digit format ("2_digits") or 3-digits format ("3_digits") [default "2_digits"].
verbose	Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

Value

Invisible data frame in genepop format

Author(s)

Custodian: Bernd Gruber (Post to https://groups.google.com/d/forum/dartr)

Examples

## Not run: 
require("dartR.data")
# SNP data
geno <- gl2genepop(testset.gl[1:3,1:9])
head(geno)
test <- gl.filter.callrate(platypus.gl,threshold = 1)
popNames(test)
gl2genepop(test, pop_order = c("TENTERFIELD","SEVERN_ABOVE","SEVERN_BELOW"),
           output_format="3_digits")

## End(Not run)

dartR documentation built on April 4, 2025, 12:23 a.m.